Cryptodynamic 18 Sep 2015 14:23
It looks like killing the Vine Confluence, whether through the Massive Flower choice encounter or the combat encounter, removes it and the Massive Flower encounter permanently. So, even if you've unlocked that way into the Midgard facility you can still lose access; something to keep in mind. I was still able to reach the Massive Flower encounter after running into it in the combat encounter the first time, but dying and winding up with energy of Parasitic Vine, though, so it seems like just angering it by chopping vines isn't enough to lock you out.